Axonal myelination is an important indicator of brain development and is implicated in many neurologic diseases. However, MRI methods to probe myelin are sensitive but not specific. Small-angle X-ray scattering (SAXS) produces signal specific to myelin’s nanostructural periodicity. Here we apply the recently developed SAXS tensor tomography (SAXS-TT) to non-invasively retrieve myelin levels in mouse brains, and compare them to myelin-sensitive MRI methods. We demonstrate SAXS-TT myelin specificity i) using myelin histology, ii) on a dysmyelination model and iii) by selectively probing central and peripheral nervous system myelin. We propose SAXS-TT as quantitative tomographic method for validating MRI myelin-sensitive sequences.